Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and Web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases and Web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research

Dwelling on ontology - semantic reasoning over topographic maps

The thesis builds upon the hypothesis that the spatial arrangement of topographic features, such as buildings, roads and other land cover parcels, indicates how land is used. The aim is to make this kind of high-level semantic information explicit within topographic data. There is an increasing need to share and use data for a wider range of purposes, and to make data more definitive, intelligent and accessible. Unfortunately, we still encounter a gap between low-level data representations and high-level concepts that typify human qualitative spatial reasoning. The thesis adopts an ontological approach to bridge this gap and to derive functional information by using standard reasoning mechanisms offered by logic-based knowledge representation formalisms. It formulates a framework for the processes involved in interpreting land use information from topographic maps. Land use is a high-level abstract concept, but it is also an observable fact intimately tied to geography. By decomposing this relationship, the thesis correlates a one-to-one mapping between high-level conceptualisations established from human knowledge and real world entities represented in the data. Based on a middle-out approach, it develops a conceptual model that incrementally links different levels of detail, and thereby derives coarser, more meaningful descriptions from more detailed ones. The thesis verifies its proposed ideas by implementing an ontology describing the land use ‘residential area’ in the ontology editor Protégé. By asserting knowledge about high-level concepts such as types of dwellings, urban blocks and residential districts as well as individuals that link directly to topographic features stored in the database, the reasoner successfully infers instances of the defined classes. Despite current technological limitations, ontologies are a promising way forward in the manner we handle and integrate geographic data, especially with respect to how humans conceptualise geographic space

A GENERIC ARCHITECTURE FOR INSIDER MISUSE MONITORING IN IT SYSTEMS

Intrusion Detection Systems (IDS) have been widely deployed within many organisations' IT nenvorks to delect network penetration attacks by outsiders and privilege escalation attacks by insiders. However, traditional IDS are ineffective for detecting o f abuse o f legitimate privileges by authorised users within the organisation i.e. the detection of misfeasance. In essence insider IT abuse does not violate system level controls, yet violates acceptable usage policy, business controls, or code of conduct defined by the organisation. However, the acceptable usage policy can vary from one organisation to another, and the acceptability o f user activities can also change depending upon the user(s), application, machine, data, and other contextual conditions associated with the entities involved. The fact that the perpetrators are authorised users and that the insider misuse activities do not violate system level controls makes detection of insider abuse more complicated than detection o f attacks by outsiders. The overall aim o f the research is to determine novel methods by which monitoring and detection may be improved to enable successful detection of insider IT abuse. The discussion begins with a comprehensive investigation o f insider IT misuse, encompassing the breadth and scale of the problem. Consideration is then given to the sufficiency of existing safeguards, with the conclusion that they provide an inadequate basis for detecting many o f the problems. This finding is used as the justification for considering research into alternative approaches. The realisation of the research objective includes the development of a taxonomy for identification o f various levels within the system from which the relevant data associated with each type of misuse can be collected, and formulation of a checklist for identification of applications that requires misfeasor monitoring. Based upon this foundation a novel architecture for monitoring o f insider IT misuse, has been designed. The design offers new analysis procedures to be added, while providing methods to include relevant contextual parameters from dispersed systems for analysis and reference. The proposed system differs from existing IDS in the way that it focuses on detecting contextual misuse of authorised privileges and legitimate operations, rather than detecting exploitation o f network protocols and system level \ailnerabilities. The main concepts of the new architecture were validated through a proof-of-concept prototype system. A number o f case scenarios were used to demonstrate the validity of analysis procedures developed and how the contextual data from dispersed databases can be used for analysis of various types of insider activities. This helped prove that the existing detection technologies can be adopted for detection o f insider IT misuse, and that the research has thus provided valuable contribution to the domain

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Corpus linguistics for the exploration of legal precedent

A deterioration of legal research skills has become a critical issue for lawyers. This thesis examines the causes of the problem under English law and specifically addresses how current technology for legal research contributes to or ameliorates the skills deficit. England has a "common law" system where the state of the law is determined by precedents laid down in previous cases. This linkage between cases means that lawyers have to assimilate a large amount of written language in order to understand the key elements of prior judgements. There are approximately two million criminal cases and another two million civil cases heard in England each year, from which the important decisions are reported. This thesis first analyses the way in which lawyers work in conducting legal research. The findings indicate that the move online has improved access to legal information but it has compromised the ability of practitioners to identify high-quality precedent and to discard information which is not relevant. A side-effect is the marginalisation of trained law librarians and their curation skills which contributes to the problem. Existing platforms prioritise comprehensive data coverage over delivering a curated research environment. A need to better train lawyers in the skills of critical thinking and linguistic analysis through computer-based tools is identified. This thesis proposes that linguistic analysis techniques from the domain of corpus linguistics can help. Single-context legal research tools which minimise the need to switch between different applications are also required. Effective working is currently compromised by having to navigate between many different tools. The development of effective collaboration skills is of particular importance. Lawyers must work well in teams in order to prepare cases effectively. The Legal Research and Collaboration platform is the prototype application which results from this research. It is a software system for legal research within teams of lawyers. Experiments establish how effectively LARC works for both practising lawyers and for law students. A foundation for future work is laid because the software is entirely open source and is based upon open access legal data. The results show that critical barriers which result in poor legal research skills can be ameliorated by well-designed computer-based tools

Intuitive interaction: Steps towards an integral understanding of the user experience in interaction design

A critical review of traditional practices and methodologies demonstrates an underplaying of firstly the role of emotions and secondly aspects of exploration in interaction behaviour in favour of a goal orientated focus in the user experience (UX). Consequently, the UX is a commodity that can be designed, measured, and predicted. An integral understanding of the UX attempts to overcome the rationalistic and instrumental mindset of traditional Human-Computer Interaction (HCI) on several levels. Firstly, the thesis seeks to complement a functional view of interaction with a qualitative one that considers the complexity of emotions. Emotions are at the heart of engagement and connect action irreversibly to the moment it occurs; they are intettwined with cognition, and decision making. Furthermore, they introduce the vague and ambiguous aspects of experience and open it up to potentiality of creation. Secondly, the thesis examines the relationship between purposive and non-purposive user behaviour such as exploration, play and discovery. The integral position proposed here stresses the procedurally relational nature and complexity of interaction experience. This requires revisiting and augmenting key themes of HCI practice such as interactivity and intuitive design. Intuition is investigated as an early and unconscious form of learning, and unstructured browsing discussed as random interaction mechanisms as forms of implicit learning. Interactivity here is the space for user's actions, contributions and creativity, not only in the design process but also during interaction as co-authors of their experiences. Finally, I envisage integral forms of usability methods to embrace the vague and the ambiguous, in order to enrich HCI's vocabulary and design potential. Key readings that inform this position cut across contemporary philosophy, media and interaction studies and professional HCI literature. On a practical level, a series of experimental interaction designs for web-browsing aim to augment the user's experience, and create space for user's intuition

B!SON: A Tool for Open Access Journal Recommendation

Finding a suitable open access journal to publish scientific work is a complex task: Researchers have to navigate a constantly growing number of journals, institutional agreements with publishers, funders’ conditions and the risk of Predatory Publishers. To help with these challenges, we introduce a web-based journal recommendation system called B!SON. It is developed based on a systematic requirements analysis, built on open data, gives publisher-independent recommendations and works across domains. It suggests open access journals based on title, abstract and references provided by the user. The recommendation quality has been evaluated using a large test set of 10,000 articles. Development by two German scientific libraries ensures the longevity of the project